Courage
by Inevitable318
Summary: A twist from the original story. What would have happened if Shinji Ikari found out the truth about the Human Instrumentality Project?
1. Prologue  Confidential

**Courage  
**

**  
**

_Only when we are no longer afraid do we begin to live. - Dorothy Thompson  
_

Disclaimer: I do not own Evangelion nor its characters.  


**Prologue - Confidential**

Gendo Ikari stepped across the threshold leading to the confines of Terminal Dogma, followed closely by his second in command, Kozo Fuyutsuki. As they boarded the elevator that will take them into the deepest reaches of NERV's facilities, Gendo Ikari asked,

"Has the third child been contacted?"

Turning to his companion, Fuyutsuki answered,

"He will be arriving today. Must you refer to your own son with such indifferent formality?"

"Transfer all guardianship to Misato Katsuragi upon his arrival and prepare him for synchronization with Unit 01." replied Ikari, blatantly ignoring the posed question.

Sub Commander Fuyutsuki nodded in acknowledgement and stepped off the elevator after Commander Ikari, entering the vast cell known as Terminal Dogma.

The supposed cell was not orthodox in the least. There were no bars, just a vast empty room save for the colossal figure at the far end of the room. There stood the mother of all humans, Lilith, impaled by a giant lance through its torso and into a crucifix as tall as the angel itself. The entry point of the lance did not leave a mark. In fact, unseemingly as it sounds, one would have guessed that the angel bore no wound whatsoever from the protruding lance save for the perpetual flow of a yellow-tinted, translucent liquid seeping from the impaling point of the lance. This liquid, known as LCL (Link Connect Liquid), ran down the massive white body of the angel and into a lake, formed soley by the gradual discharge of this liquid from the angel itself.

As he glanced up at the lifeless form of the second angel, Lilith, Commander Ikari decided they were safe enough from the risk of listening ears.

"The agenda is complete. The old men of SEELE believe we are at their disposal. The Human Instrumentality Project will commence as we have planned."

At this, the older of the two - Fuyutsuki asked, "Will it be enough? The slightest mistake will betray our intentions to the old men. What then?"

Turning from the giant figure, Commander Ikari adjusted his shaded glasses and faced his subordinate.

"Irrelevant. Mistakes will not be tolerated nor will they be allowed to occur. Absolute secrecy will ensure our success. Nothing else matters. The two people standing in this room are the only ones that know of our intentions. Make sure it stays that way Fuyutsuki."

It was at this moment that the siren announcing the arrival of an angel blared for the very first time...

A/N - This is my first Fanfic. Any feedback will be welcome! Thanks!


	2. Chapter 1  Acquaintance

**Courage  
**

**  
**

_Only when we are no longer afraid do we begin to live. - Dorothy Thompson  
_

Disclaimer: I do not own Evangelion nor its characters.  


A/N - Fast-forward to the morning after Operation Yashima during which Shinji receives Rei's first smile.

**Chapter 1 - Acquaintance**

Shinji Ikari woke up with a faint smile on his face. He had seen Rei Ayanami smile for the first time for him the previous evening. Still wearing the smile on his face, he gathered up his clothes and headed to the bathroom to take a shower. After his daily morning-hygiene routine, he stepped into the kitchen eagerly expecting to see breakfast waiting for him, for it was Misato's turn to cook that morning.

...what was he thinking?

As he entered the kitchen, Pen-Pen waddled out of his "room" and proceeded to gesture wildly at the refrigerator. Sighing inwardly, Shinji dropped a couple slices of bread in the toaster and retrieved some fish out of the refrigerator for Pen-Pen. It wouldn't hurt to actually keep her word once in a while about the chore schedule that _she_ had come up with, would it? Was he asking too much?

This thought was crossing through Shinji's mind when Misato decided to enter the kitchen in all her glory. Clad only in underwear. Half asleep. And hung-over. Exasperated, Shinji decided that he was, indeed, asking too much. Predictably, the still groggy Misato clambered over to the refrigerator to down a can of beer.

-Gulp- -Gulp- -Gulp-

"Thaaaaaaat's the stuff! Morning Shinji!"

"Good Morning..." came the irritated reply.

It really was amazing how a can of beer can completely change a person's attitude. Now cheerful as a puppy, Misato snatched the piece of toast that was halfway to Shinji's mouth and gobbled it down. Sure. Attitudes it can change, but a can of beer apparently could not change a person's morning breath.

"Gross! Misato, go brush your teeth!"

"Sorry, sorry. I'll go take a shower in a bit," replied Misato, completely unfazed.

"There's a reason why you're still single you know...

Are you really coming to the school today?"

Today was the parent-teacher career meeting. Since Shinji's father was basically...not a father, Misato had said that she would go in his stead. Shinji however, unused to anyone coming to a parent-teacher meeting for him, was skeptical about Misato's involvement.

"Of course! It's your parent-teacher career meeting isn't it?"

"Yes, but aren't you busy?"

"Don't worry about it, it's my responsibility."

Oh.

"Responsibility..."

Well, he understood. Of course she was coming, it was a part of her job. She was obligated to come. Feeling a little down at this reply, Shinji headed into his room to grab his schoolbag, leaving a completely oblivious Misato who was busy searching for her underwear in the kitchen. Just as he left his room with his schoolbag, the doorbell rang announcing the arrival of his two friends, Kensuke Aida and Touji Suzuhara.

It was rather amusing how enthusiastic they were about coming over to Shinji's apartment to pick him up every morning. Shinji very much doubted that they came just to pick him up. Rather, it was painfully obvious that they came just to get a glimpse of Misato in the morning. Unfortunately for them, she did not grace them with her indecent presence, choosing only to stick her arm out of her room to wave them good-bye.

Brightened by the prospect of walking to school with his two friends and possibly seeing Rei Ayanami's smile once again, Shinji smiled throughout the entire trip to school - a rare sight to see for a usually gloomy boy.

---

School was a boring event. All the teacher ever did was drone on about second impact. Apparently according to his teacher, it was a meteorite only 4 inches wide that had hit the continent of Antartica at 95 of the speed of light. This seemingly small piece of rock had caused the destruction of millions of people and started a global war with countries destroying each other for food and supplies. The entire thing sounded very suspicious to Shinji. How could a rock the size of a baseball cause an explosion capable of melting the Antartic Icecaps? And if it indeed was rock that size, why didn't it disintegrate while entering the earth's atmosphere?

Still daydreaming about what might have actually caused the second impact if not for the supposed meteorite, Shinji failed to notice Misato swerving into the parking lot in her red sports car until Touji and Kensuke almost pushed him out the window rushing to get a better look at the dark haired beauty.

"Wow she's beautiful!" exclaimed Touji in blatant awe.

"Wipe the drool off your face, you haven't seen her at home...she's a complete slob." replied a clearly disinterested Shinji.

"Well, better for us, Shinji's still too much of a baby to appreciate the female figure, ain't ya Shinji?" teased Kensuke.

"You try to appreciate female figure when you see her in the morning barely dressed with her hair all over the place!" shot back Shinji, annoyed.

Touji and Kensuke stared.

"Barely dressed?" breathed out Touji.

Apparently that was the wrong thing to say, as Shinji now lay with his face smashed against the top of his desk with two very red, very visible hand marks on the rear of his head.

---

After the parent-teacher conference had ended, Shinji headed up to the roof of the school to join his two friends for lunch. It was always nice up on the roof. Since the second impact had turned Japan into a land of perpetual summer, it was hard to find a nice cool place to sit down and relax. However, the roof of Shinji's school was just perfect because it was high enough to feel the breeze blowing in from the sea, but also low enough to receive the cooling shade of the neighboring buildings. The best part was the little patch of grass on far side of the flat roof that housed two small pine trees – a perfect place to hang out during lunch.

As Shinji made his way to his friends leaning against the two trees on the roof, he was mildly surprise to find out that they had been discussing what had really happened during second impact. Shinji went over to listen as Kensuke excitedly recounted his discoveries to an apathetic Touji.

"I didn't think I could do it, but the files weren't that hard to hack!" explained Kensuke breathlessly. "Shinji! Guess what? I was able to hack into NERV's mainframe and retrieve information about the Second Impact!"

Clueless as to the workings of computer programming, Shinji asked, "Is that hard to do?"

Gaping at Shinji's lack of knowledge, Kensuke replied, "Of course! NERV has the best security system in the world! Even the world's most renowned hackers couldn't breach NERV's mainframe security system. But I got in!"

Still not sure what Kensuke was talking about, but definitely impressed, Shinji said, "So what did you find?"

As if he was waiting for someone to ask, Kensuke answered immediately, "Well apparently, it wasn't a meteorite at all! The files indicate that they found something called the "White Moon" near the coast of Antarctica and they sent a NERV expedition to inspect it. But get this, it was the experiments they were conducting there that caused sec-"

Before Kensuke even finished this sentence, two men in black suits burst out onto the roof, pointing their pistols at the shocked teenagers.

"Freeze! Hands in the air!"

At a loss of what to do, the three teenagers obeyed.

What was going on? Had they realized that someone had made it past their computer security system? Nervously, Shinji turned his head slightly to find a completely terror-stricken Kensuke, eyes wide with fear.

Apprehension flooded Kensuke's face as one of the men approached Kensuke and bound his hands with cuffs. Concerned but still shocked into inaction, Shinji and Touji helplessly watched as Kensuke was taken into custody.

The man that had stood back and watched his partner put the handcuffs on Kensuke now spoke into his ear piece.

"We have located and secured the target."

As his frightened friend was taken away by the two men, Shinji heard one of the men say,

"Kensuke Aida, we have some questions we'd like to ask you."

---

A/N - First chapter done! Just want to let you guys know that, from this point on, although there will be some similiarities, the characters and the plot will be developed completely differently.

Sorry that the chapter is still short! It was more or less an introduction to the deeper plot that lies ahead. Thanks:D


End file.
